The diploma thesis deals with the application of a controlling system for managing deviations in a selected company using the Activity Based Costing methodology. Within the theoretical background, we deal with the issue of controlling in terms of basic characteristics, which are at the end of the theoretical part focused on costs controlling with a link to the deviation management system. The practical part is devoted to the presentation of the company in terms of knowledge of the subject of business, the offered portfolio of products with the subsequent evaluation of the current economic situation of the company. Due to the non-existence of a comprehensive system for managing deviations in the company, we further focus on the general application of such a management system using the principles of the Activity Based Costing methodology. In the last part of the practical part, we recommend a proposal for the use of a controlling report based on the principles of calculation of variable costs.